Embryonic development is defined by the emergence of spatial patterns of gene expression, which organize progenitor cells into the blueprint of tissues and organs. To understand how genetic information gives rise to tridimensional arrangements of cells, we need to assess how genomes are regulated in space and time. While emerging technologies have allowed for precise quantification of gene expression in single cells, strategies to integrate transcriptomic information and spatial cellular heterogeneity have been lacking. Here, we propose to combine spatial transcriptomics and epigenomic profiling to reconstruct the regulatory architecture of the early amniote embryo. By conducting RNA-seq in cryo-sections of the avian embryo, we will establish a set of transcriptomic coordinates along the body axes. These parameters will allow us to position single-cell RNA-seq datasets in a tridimensional grid that will be used to reconstruct spatial patterns of gene expression on a genome-wide scale. To test this approach we assembled a prototype of this virtual embryo, which is composed of pixels containing regulatory information from all genes expressed in the genome. This model allowed us to recreate spatial expression patterns, uncovering a high degree of regulatory complexity in the chick gastrula. Since this is likely to be reflected in the genomic organization of gastrulating cells, a second aim of this proposal is to use a Cartesian approach to explore chromatin regulation in space. We will establish how chromatin accessibility and histone modifications change along the three axes of the embryo, and assemble tridimensional maps of active genomic elements. We will use these high- resolution models of the amniote gastrula to define the gene regulatory program that controls the emergence of distinct fields of progenitor cells. Ultimately, our goal is to define how the gene regulatory networks operate in space to drive pattern formation in the developing embryo.!